title: Genetic diversity and population structure of rice pathogen Ustilaginoidea virens in China.
abstract: Rice false smut caused by the fungal pathogen Ustilaginoidea virens is becoming a destructive disease throughout major rice-growing countries. Information about its genetic diversity and population structure is essential for rice breeding and efficient control of the disease. This study compared the genome sequences of two U. virens isolates. Three SNP-rich genomic regions were identified as molecular markers that could be used to analyze the genetic diversity and population structure of U. virens in China. A total of 56 multilocus sequence types (haplotypes) were identified out of 162 representative isolates from 15 provinces covering five major rice-growing areas in China. However, the phylogeny, based on sequences at individual SNP-rich regions, strongly conflicted with each other and there were significant genetic differences between different geographical populations. Gene flow between the different geographical populations and genetic differentiation within each geographical population were also detected. In addition, genetic recombination and genetic isolation resulting from geographic separation was also found.
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
authors.forename: Xianyun
authors.initials: X
authors.lastname: Sun
authors.forename: Shu
authors.initials: S
authors.lastname: Kang
authors.forename: Yongjie
authors.initials: Y
authors.lastname: Zhang
authors.forename: Xinqiu
authors.initials: X
authors.lastname: Tan
authors.forename: Yufei
authors.initials: Y
authors.lastname: Yu
authors.forename: Haiyong
authors.initials: H
authors.lastname: He
authors.forename: Xinyu
authors.initials: X
authors.lastname: Zhang
authors.forename: Yongfeng
authors.initials: Y
authors.lastname: Liu
authors.forename: Shu
authors.initials: S
authors.lastname: Wang
authors.forename: Wenxian
authors.initials: W
authors.lastname: Sun
authors.forename: Lei
authors.initials: L
authors.lastname: Cai
authors.forename: Shaojie
authors.initials: S
authors.lastname: Li
mesh_terms: D001483:Base Sequence; D001947:Breeding / Q000379:methods; D002681:China; D017931:DNA Primers / Q000235:genetics; D003710:Demography; D051456:Gene Flow / Q000235:genetics*; D014644:Genetic Variation; D005828:Genetics, Population; D006239:Haplotypes / Q000235:genetics; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012275:Oryza / Q000382:microbiology*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014587:Ustilaginales / Q000235:genetics*
chemical_list: D017931:DNA Primers